library(httr)
library(jsonlite)
library(countrycode)
library(janitor)
library(readxl)
library(sf)
sf_use_s2(FALSE)
library(tmap)
tmap_mode('view')
library(tidyverse)
options(knitr.kable.NA = '')Data cleaning and auditing
Data cleaning
Read data
raw_metadata <- read_xlsx('data/metada_work_version.xlsx', guess_max = 4000) Check columns
raw_metadata <- raw_metadata %>%
janitor::clean_names() %>%
janitor::remove_empty(c('rows', 'cols')) Check source fields
The fields are: name_orig, format, and language.
- Make sure there are no
\r,\n, other weird characters or typos. - Capitalise and clean
language.
# name
raw_metadata %>%
filter(grepl('http', name_orig)) %>%
group_by(name_orig) %>% count
raw_metadata %>%
mutate(name_orig = str_squish(name_orig)) %>%
mutate(name_orig = str_remove_all(name_orig, "\\\\")) %>%
mutate(name_orig = str_remove_all(name_orig, "\"")) %>%
group_by(name_orig) %>%
summarise(n_countries = n_distinct(country)) %>%
select(name_orig, n_countries) %>%
print(n=10)
# format
raw_metadata %>%
mutate(format = ifelse(format == 'NA', NA, str_squish(format))) %>%
distinct(format)
# language
raw_metadata %>%
mutate(language = ifelse(language == 'NA', NA, str_squish(language))) %>%
mutate(language = str_replace(language, "/|\\|", ' | ')) %>%
distinct(language) %>%
print(n=50)DOUBTS
The name_orig is: https://www.odonat-grandest.fr/listes-rouges-grand-est-etat-avancement/.
The id values are: [1] 446 447 448 449 450 451 452 453 454 455 456 457.
FIX
# French: Liste rouge des Amphibiens du Grand Est
# English: Red list of Mammals of Grand Est
raw_metadata %>%
mutate(name_orig = ifelse(grepl('htt', name_orig) &
state_province == 'Grand Est',
str_glue('Red list of {group} of Grand Est'), name_orig)) %>%
filter(state_province == 'Grand Est') %>% select(group, name_orig)
raw_metadata %>%
mutate(language = ifelse(language == 'NA', NA, str_squish(language))) %>%
mutate(language = str_replace(language, "/|\\|", ' | '))
raw_metadata %>%
mutate(format = ifelse(format == '?', NA, format))
raw_metadata %>%
mutate(name_orig = str_squish(name_orig)) %>%
mutate(name_orig = str_remove_all(name_orig, "\\\\")) %>%
mutate(name_orig = str_remove_all(name_orig, "\"")) Check Location fields
The fields are: continent, country, state_province, gadm_level_1, gadm_level_2, region_custom, region_detail, and iso_2.
- Make sure there are no typos, thus duplicates.
- Capitalise
continent,country,state_provincenames.
- Check ISO codes.
- Check GADM levels.
- Clean
region_customandregion_detail.
# check continent
raw_metadata %>%
mutate(continent = str_squish(str_replace_all(str_squish(continent), '\\|', ' | '))) %>%
mutate(continent = str_replace_all(continent, '_', ' ')) %>%
mutate(continent = str_to_title(continent)) %>%
distinct(continent)
# check country
raw_metadata %>%
mutate(country = ifelse(country == 'NA', NA, str_squish(country))) %>%
mutate(country = str_replace_all(country, '_', ' ')) %>%
mutate(country = ifelse(country == 'USSR', country, str_to_title(country))) %>%
mutate(country = str_replace_all(country, 'And ', 'and ')) %>%
mutate(country = str_replace_all(country, 'Of', 'of')) %>%
mutate(country = str_replace_all(country, 'The', 'the')) %>%
distinct(country)
# check state_province
raw_metadata %>%
mutate(state_province = ifelse(state_province == 'NA', NA, str_squish(state_province))) %>%
mutate(state_province = str_to_title(state_province)) %>%
mutate(state_province = str_replace_all(state_province, 'And ', 'and ')) %>%
mutate(state_province = str_replace_all(state_province, 'Of', 'of')) %>%
mutate(state_province = str_replace_all(state_province, 'The', 'the')) %>%
filter(!is.na(state_province)) %>%
filter(state_province != gadm_level_1) %>%
distinct(country, state_province, gadm_level_1, iso_2, iso_3) %>%
print(n=100)
# check gadm_level_1 and gadm_level_2
raw_metadata %>%
mutate(gadm_level_1 = ifelse(gadm_level_1 == 'NA', NA, str_squish(gadm_level_1))) %>%
mutate(gadm_level_1 = str_to_title(gadm_level_1)) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'And ', 'and ')) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'Of', 'of')) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'The', 'the')) %>%
filter(!is.na(gadm_level_1)) %>% distinct(gadm_level_1) %>%
arrange(gadm_level_1) %>% print(n=100)
raw_metadata %>%
mutate(gadm_level_2 = ifelse(gadm_level_2 == 'NA', NA, str_squish(gadm_level_2))) %>%
mutate(gadm_level_2 = str_to_title(gadm_level_2)) %>%
filter(!is.na(gadm_level_2)) %>% select(gadm_level_2)
# check region_custom and region_detal
raw_metadata %>%
mutate(region_custom = ifelse(region_custom == 'NA', NA, str_squish(region_custom))) %>%
mutate(region_detail = ifelse(region_detail == 'NA', NA, str_squish(region_detail))) %>%
mutate(region_detail = str_squish(str_replace_all(str_squish(region_detail), '\\|', ' | '))) %>%
filter(!is.na(region_custom)) %>%
distinct(region_custom, region_detail, iso_2, iso_3) %>%
print(n=100)
# check iso_2 and iso_3
raw_metadata %>%
janitor::clean_names() %>%
janitor::remove_empty(c('rows', 'cols')) %>%
mutate(iso_2 = ifelse(iso_2 == 'NA' & country != 'Namibia', NA, str_squish(iso_2))) %>%
mutate(iso_2 = str_squish(str_replace_all(str_squish(iso_2), '\\|', ' | '))) %>%
mutate(iso_3 = ifelse(iso_3 == 'NA', NA, str_squish(iso_3))) %>%
mutate(iso_3 = str_squish(str_replace_all(str_squish(iso_3), '\\|', ' | '))) %>%
select(country, iso_2, iso_3, region_custom, region_detail) %>%
filter(is.na(iso_2)) #%>% distinct()DOUBTS
Check Taxon fields
The fields are: kingdom, phylum, subphylum, class, order, and group.
- Check duplicates in all fields.
- Rename
grouptotaxa.
I searched names using the GBIF backbone, using my own custom function nameMatcherGBIF().
# gbif name parser
nameMatcherGBIF <- function(sp_name_list) {
# api <- 'http://api.gbif.org/v1/parser/name'
api <- 'http://api.gbif.org/v1/species/match'
name_parsed <- tibble(sp_name = character(),
scientificName = character(),
kingdom = character(),
phylum = character(),
class = character(),
order = character(),
family = character(),
genus = character(),
specificEpithet = character(),
species = character(),
status = character(),
rank = character())
for(sp_name in sp_name_list){
# cat(sp_name, '\n')
call_url <- str_glue('{api}?name={sp_name}&strict=true&verbose=false')
get_json_call <- GET(url = URLencode(call_url)) %>%
content(as = "text") %>% fromJSON(flatten = TRUE)
if(get_json_call$matchType == 'NONE') {
name_parsed_i <- tibble(sp_name = sp_name,
scientificName = NA,
kingdom = NA,
phylum = NA,
class = NA,
order = NA,
family = NA,
genus = NA,
specificEpithet = NA,
species = NA,
status = NA,
rank = NA)
name_parsed <- rbind(name_parsed, name_parsed_i)
} else{
name_parsed_i <- tibble(sp_name = sp_name,
scientificName = ifelse(exists('scientificName',get_json_call), get_json_call$scientificName, NA),
kingdom = ifelse(exists('kingdom',get_json_call), get_json_call$kingdom, NA),
phylum = ifelse(exists('phylum',get_json_call), get_json_call$phylum, NA),
class = ifelse(exists('class',get_json_call), get_json_call$class, NA),
order = ifelse(exists('order',get_json_call), get_json_call$order, NA),
family = ifelse(exists('family',get_json_call), get_json_call$family, NA),
genus = ifelse(exists('genus',get_json_call), get_json_call$genus, NA),
specificEpithet = ifelse(exists('specificEpithet',get_json_call), get_json_call$specificEpithet, NA),
species = ifelse(exists('species',get_json_call), get_json_call$species, NA),
status = ifelse(exists('status',get_json_call), get_json_call$status, NA),
rank = ifelse(exists('rank',get_json_call), get_json_call$rank, NA))
name_parsed <- rbind(name_parsed, name_parsed_i)
}
}
return(name_parsed)
}
sp_list <- raw_metadata %>%
distinct(kingdom, phylum, subphylum, class, order, group) %>%
mutate(group = str_trim(group)) %>%
mutate(group = str_to_title(group)) %>%
mutate(group = str_replace_all(group, 'And ', 'and ')) %>%
mutate(group = str_replace_all(group, 'Of', 'of')) %>%
mutate(group = str_replace_all(group, 'The', 'the')) %>%
pull(group)
sp_list_matched <- nameMatcherGBIF(sp_list) %>% suppressMessages()
sp_list_matched <- sp_list_matched %>%
mutate(scientificName = case_when(grepl('flora', sp_name, ignore.case=T) ~ 'Plantae',
grepl('fauna', sp_name, ignore.case=T) ~ 'Animalia',
grepl('tunicata', sp_name, ignore.case=T) ~ NA,
.default = scientificName)) %>%
mutate(kingdom = case_when(grepl('flora', sp_name, ignore.case=T) ~ 'Plantae',
grepl('fauna', sp_name, ignore.case=T) ~ 'Animalia',
grepl('tunicata', sp_name, ignore.case=T) ~ NA,
.default = kingdom)) %>%
mutate(phylum = ifelse(phylum == 'chordata', 'Chordata', phylum))
sp_list_unmatched <- sp_list_matched %>%
filter(is.na(scientificName)) %>% pull(sp_name)
sp_list_matched %>% filter(!is.na(kingdom)) %>% nrow() # matched[1] 205
length(sp_list_unmatched) # not matched[1] 358
When the taxon name (i.e., group) was not found I kept the previous taxonomic fields’ values.
merged_list <- left_join(raw_metadata %>%
mutate(group = str_trim(group)) %>%
distinct(group) %>%
arrange(group),
sp_list_matched %>%
filter(!is.na(scientificName)) %>%
rename(group=sp_name) %>% distinct()) %>%
arrange(group)
raw_metadata_taxon_list <- raw_metadata %>%
mutate(group = str_trim(group)) %>%
distinct(group, .keep_all = T) %>%
select(kingdom, phylum, subphylum, class, order, group) %>%
arrange(group)
left_join(raw_metadata %>% mutate(group = str_trim(group)) %>%
select(-c(kingdom,phylum,subphylum,class,order)),
bind_rows(merged_list %>%
filter(!is.na(scientificName)),
merged_list %>%
filter(is.na(scientificName)) %>%
select(group) %>%
left_join(. , raw_metadata_taxon_list))) %>%
mutate(group = str_trim(group)) %>%
mutate(group = str_to_title(group)) %>%
mutate(group = str_replace_all(group, 'And ', 'and ')) %>%
mutate(group = str_replace_all(group, 'Of', 'of')) %>%
mutate(group = str_replace_all(group, 'The', 'the')) %>%
mutate(group = str_replace_all(group, 'Et Al.', 'et al.')) %>%
distinct(group, kingdom, phylum, class, order, family, rank) %>%
arrange(kingdom, phylum, class, order) %>%
kableExtra::kbl(booktabs = T) %>%
kableExtra::kable_styling(latex_options = c('striped', 'hold_position'))| group | kingdom | phylum | class | order | family | rank |
|---|---|---|---|---|---|---|
| Earthworms | Animalia | Anelida | Clitellata | Opisthopora | ||
| Oligochaeta | Animalia | Anelida | Clitellata | |||
| Onychophora | Animalia | Animalia | ||||
| Branchiobdellida | Animalia | Annelida | Clitellata | Branchiobdellida | ORDER | |
| Hirudinea | Animalia | Annelida | Clitellata | |||
| Worms | Animalia | Annelida | Clitellata | |||
| Leech | Animalia | Annelida | Clitellata | |||
| Leeches | Animalia | Annelida | Clitellata | |||
| Echiurida | Animalia | Annelida | Echiura | Echiuroidea | ||
| Sipunculids | Animalia | Annelida | Sipuncula | |||
| Amblypygi | Animalia | Arthropoda | Arachnida | Amblypygi | ORDER | |
| Spiders | Animalia | Arthropoda | Arachnida | Araneae | ||
| Uropodina | Animalia | Arthropoda | Arachnida | Mesostigmata | ||
| Opiliones | Animalia | Arthropoda | Arachnida | Opiliones | ORDER | |
| Opilioness | Animalia | Arthropoda | Arachnida | Opiliones | ||
| Pseudoscorpiones | Animalia | Arthropoda | Arachnida | Pseudoscorpiones | ORDER | |
| False Scorpions | Animalia | Arthropoda | Arachnida | Pseudoscorpions | ||
| Scorpions | Animalia | Arthropoda | Arachnida | Scorpionida | ||
| Arachnida | Animalia | Arthropoda | Arachnida | CLASS | ||
| Anostraca | Animalia | Arthropoda | Branchiopoda | Anostraca | ORDER | |
| Branchiopoda | Animalia | Arthropoda | Branchiopoda | CLASS | ||
| Centipedes | Animalia | Arthropoda | Chilopoda | |||
| Chilopoda | Animalia | Arthropoda | Chilopoda | CLASS | ||
| Collembola | Animalia | Arthropoda | Collembola | CLASS | ||
| Entomostraca | Animalia | Arthropoda | Copepoda | |||
| Copepoda | Animalia | Arthropoda | Copepoda | CLASS | ||
| Millipedes | Animalia | Arthropoda | Diplopoda | |||
| Diplopoda | Animalia | Arthropoda | Diplopoda | CLASS | ||
| Archaeognatha | Animalia | Arthropoda | Insecta | Archaeognatha | ORDER | |
| Blattodea | Animalia | Arthropoda | Insecta | Blattodea | ORDER | |
| Wood Cockroaches | Animalia | Arthropoda | Insecta | Blattodea | ||
| Cockroaches | Animalia | Arthropoda | Insecta | Blattodea | ||
| Hydraenidae | Animalia | Arthropoda | Insecta | Coleoptera | Hydraenidae | FAMILY |
| Coleoptera | Animalia | Arthropoda | Insecta | Coleoptera | ORDER | |
| Carabidae | Animalia | Arthropoda | Insecta | Coleoptera | Carabidae | FAMILY |
| Saproxylic Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Longhorn and Scarab Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Longhorn Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Scarabaeidae | Animalia | Arthropoda | Insecta | Coleoptera | Scarabaeidae | FAMILY |
| Ladybugs | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Water Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Tenebrionidae | Animalia | Arthropoda | Insecta | Coleoptera | Tenebrionidae | FAMILY |
| Soldier Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Leaf Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Histeridae | Animalia | Arthropoda | Insecta | Coleoptera | Histeridae | FAMILY |
| Sphaeritidae | Animalia | Arthropoda | Insecta | Coleoptera | Sphaeritidae | FAMILY |
| Derodontidoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Bostrichoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Staphylinidae | Animalia | Arthropoda | Insecta | Coleoptera | Staphylinidae | FAMILY |
| Lucanidae | Animalia | Arthropoda | Insecta | Coleoptera | Lucanidae | FAMILY |
| Geotrupidae | Animalia | Arthropoda | Insecta | Coleoptera | Geotrupidae | FAMILY |
| Trogidae | Animalia | Arthropoda | Insecta | Coleoptera | Trogidae | FAMILY |
| Silphidae | Animalia | Arthropoda | Insecta | Coleoptera | Silphidae | FAMILY |
| Chrysomelidae | Animalia | Arthropoda | Insecta | Coleoptera | Chrysomelidae | FAMILY |
| Bark Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Ground Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Curculionidae | Animalia | Arthropoda | Insecta | Coleoptera | Curculionidae | FAMILY |
| Powderpost Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Bostrichidae | Animalia | Arthropoda | Insecta | Coleoptera | Bostrichidae | FAMILY |
| Anobiidae | Animalia | Arthropoda | Insecta | Coleoptera | Anobiidae | FAMILY |
| Ptinidae | Animalia | Arthropoda | Insecta | Coleoptera | Ptinidae | FAMILY |
| Deadwood Beetle | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Buprestidae | Animalia | Arthropoda | Insecta | Coleoptera | Buprestidae | FAMILY |
| Snout Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Staphylinoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Cucujoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Lamellicornia | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Seed Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Weevils | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Anthribidae | Animalia | Arthropoda | Insecta | Coleoptera | Anthribidae | FAMILY |
| Platypodidae | Animalia | Arthropoda | Insecta | Coleoptera | Curculionidae | FAMILY |
| Ground Beetle | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Tiger Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Megalopodidae | Animalia | Arthropoda | Insecta | Coleoptera | Megalopodidae | FAMILY |
| Scarabaeoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Cerambycidae | Animalia | Arthropoda | Insecta | Coleoptera | Cerambycidae | FAMILY |
| Curculionoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Cleroidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Elateridae | Animalia | Arthropoda | Insecta | Coleoptera | Elateridae | FAMILY |
| Lymexyloidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Cicindelidae | Animalia | Arthropoda | Insecta | Coleoptera | Carabidae | FAMILY |
| Lucanoidea | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Hydrophilidae | Animalia | Arthropoda | Insecta | Coleoptera | Hydrophilidae | FAMILY |
| Platypsyllinae | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Cholevinae | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Malachiidae | Animalia | Arthropoda | Insecta | Coleoptera | Malachiidae | FAMILY |
| Melyridae | Animalia | Arthropoda | Insecta | Coleoptera | Melyridae | FAMILY |
| Phloeophilidae | Animalia | Arthropoda | Insecta | Coleoptera | Phloiophilidae | FAMILY |
| Cleridae | Animalia | Arthropoda | Insecta | Coleoptera | Cleridae | FAMILY |
| Cerophytidae | Animalia | Arthropoda | Insecta | Coleoptera | Cerophytidae | FAMILY |
| Eucnemidae | Animalia | Arthropoda | Insecta | Coleoptera | Eucnemidae | FAMILY |
| Cryptophagidae | Animalia | Arthropoda | Insecta | Coleoptera | Cryptophagidae | FAMILY |
| Latridiidae | Animalia | Arthropoda | Insecta | Coleoptera | Latridiidae | FAMILY |
| Mycetophagidae | Animalia | Arthropoda | Insecta | Coleoptera | Mycetophagidae | FAMILY |
| Zopheridae | Animalia | Arthropoda | Insecta | Coleoptera | Zopheridae | FAMILY |
| Monotomidae | Animalia | Arthropoda | Insecta | Coleoptera | Monotomidae | FAMILY |
| Phalacridae | Animalia | Arthropoda | Insecta | Coleoptera | Phalacridae | FAMILY |
| Pyrochroide | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Meloidae | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Orsodacnidae | Animalia | Arthropoda | Insecta | Coleoptera | Orsodacnidae | FAMILY |
| Donaciinae | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Leptinidae | Animalia | Arthropoda | Insecta | Coleoptera | Leiodidae | FAMILY |
| Lissomidae | Animalia | Arthropoda | Insecta | Coleoptera | Elateridae | FAMILY |
| Derodontoidae | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Leiodidae | Animalia | Arthropoda | Insecta | Coleoptera | Leiodidae | FAMILY |
| Oedemeridae | Animalia | Arthropoda | Insecta | Coleoptera | Oedemeridae | FAMILY |
| Melandryidae | Animalia | Arthropoda | Insecta | Coleoptera | Melandryidae | FAMILY |
| Dung Beetles | Animalia | Arthropoda | Insecta | Coleoptera | ||
| Earwigs | Animalia | Arthropoda | Insecta | Dermaptera | ||
| Heteroptera | Animalia | Arthropoda | Insecta | Diptera | Sphaeroceridae | GENUS |
| Acalyptratae | Animalia | Arthropoda | Insecta | Diptera | ||
| Calypterate | Animalia | Arthropoda | Insecta | Diptera | ||
| Larger Brachycera | Animalia | Arthropoda | Insecta | Diptera | ||
| Dolichopodid | Animalia | Arthropoda | Insecta | Diptera | ||
| Lonchopteridae | Animalia | Arthropoda | Insecta | Diptera | Lonchopteridae | FAMILY |
| Platypezidae | Animalia | Arthropoda | Insecta | Diptera | Platypezidae | FAMILY |
| Opetiidae | Animalia | Arthropoda | Insecta | Diptera | Opetiidae | FAMILY |
| Hoverflies | Animalia | Arthropoda | Insecta | Diptera | ||
| Chaoboridae | Animalia | Arthropoda | Insecta | Diptera | Chaoboridae | FAMILY |
| Thaumaleidae | Animalia | Arthropoda | Insecta | Diptera | Thaumaleidae | FAMILY |
| Ceratopogonidae | Animalia | Arthropoda | Insecta | Diptera | Ceratopogonidae | FAMILY |
| Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Asilidae | Animalia | Arthropoda | Insecta | Diptera | Asilidae | FAMILY |
| Psychodidae | Animalia | Arthropoda | Insecta | Diptera | Psychodidae | FAMILY |
| Dixidae | Animalia | Arthropoda | Insecta | Diptera | Dixidae | FAMILY |
| Soldier Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Horse-Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Bee Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Empididae | Animalia | Arthropoda | Insecta | Diptera | Empididae | FAMILY |
| Conopidae | Animalia | Arthropoda | Insecta | Diptera | Conopidae | FAMILY |
| Chironomidae | Animalia | Arthropoda | Insecta | Diptera | Chironomidae | FAMILY |
| Dolichopodidae | Animalia | Arthropoda | Insecta | Diptera | Dolichopodidae | FAMILY |
| Black Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Long-Legged Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Micropezidae | Animalia | Arthropoda | Insecta | Diptera | Micropezidae | FAMILY |
| Grass Flies | Animalia | Arthropoda | Insecta | Diptera | ||
| Tachinidae | Animalia | Arthropoda | Insecta | Diptera | Tachinidae | FAMILY |
| Aquatic Empididae | Animalia | Arthropoda | Insecta | Diptera | ||
| Pediciidae | Animalia | Arthropoda | Insecta | Diptera | Pediciidae | FAMILY |
| Limoniidae | Animalia | Arthropoda | Insecta | Diptera | Limoniidae | FAMILY |
| Diptera | Animalia | Arthropoda | Insecta | Diptera | ||
| Parasitic Diptera | Animalia | Arthropoda | Insecta | Diptera | ||
| Mayflies | Animalia | Arthropoda | Insecta | Ephemeroptera | ||
| Auchenorrhyncha | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Cicadas | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Shieldbugs | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Clavicornia | Animalia | Arthropoda | Insecta | Hemiptera | Aradidae | GENUS |
| Big-Eyed Bugs | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Nepomorpha | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Fulgoromorpha | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Cicadomorpha | Animalia | Arthropoda | Insecta | Hemiptera | Palaeontinidae | GENUS |
| Scale Insect | Animalia | Arthropoda | Insecta | Hemiptera | ||
| Hemiptera | Animalia | Arthropoda | Insecta | Hemiptera | ORDER | |
| Ants | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Bombus Spp. | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Hymenoptera | Animalia | Arthropoda | Insecta | Hymenoptera | ORDER | |
| Bees | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Diversicornia | Animalia | Arthropoda | Insecta | Hymenoptera | Encyrtidae | GENUS |
| Sawflies | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Spheciformes | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Pompilidae | Animalia | Arthropoda | Insecta | Hymenoptera | Pompilidae | FAMILY |
| Chrysididae | Animalia | Arthropoda | Insecta | Hymenoptera | Chrysididae | FAMILY |
| Scolioidea | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Cuckoo Wasp | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Wasps | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Sphecidae | Animalia | Arthropoda | Insecta | Hymenoptera | Sphecidae | FAMILY |
| Wild Bees | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Scoliidae | Animalia | Arthropoda | Insecta | Hymenoptera | Scoliidae | FAMILY |
| Crabronidae et al. | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Chrysididae et al. | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Symphyta | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Stinging Wasps | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Mutillidae | Animalia | Arthropoda | Insecta | Hymenoptera | Mutillidae | FAMILY |
| Sapygidae | Animalia | Arthropoda | Insecta | Hymenoptera | Sapygidae | FAMILY |
| Tiphiidae | Animalia | Arthropoda | Insecta | Hymenoptera | Tiphiidae | FAMILY |
| Cimbicidae | Animalia | Arthropoda | Insecta | Hymenoptera | Cimbicidae | FAMILY |
| Siricidae | Animalia | Arthropoda | Insecta | Hymenoptera | Siricidae | FAMILY |
| Xiphydriidae | Animalia | Arthropoda | Insecta | Hymenoptera | Xiphydriidae | FAMILY |
| Ampulicidae | Animalia | Arthropoda | Insecta | Hymenoptera | Ampulicidae | FAMILY |
| Crabronidae | Animalia | Arthropoda | Insecta | Hymenoptera | Crabronidae | FAMILY |
| Apoidea | Animalia | Arthropoda | Insecta | Hymenoptera | ||
| Lepidoptera | Animalia | Arthropoda | Insecta | Lepidoptera | ORDER | |
| Moths | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Butterflies | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Papilionoidea | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Hesperioidea | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Noctuidae | Animalia | Arthropoda | Insecta | Lepidoptera | Noctuidae | FAMILY |
| Night Butterflies | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Owlet Moths | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Lymantriinae | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Short-Cloaked Moth | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Geometer Moths | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Bombyces | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Sphinges S.l. | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Pyralidae | Animalia | Arthropoda | Insecta | Lepidoptera | Pyralidae | FAMILY |
| Sphinges | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Geometridae | Animalia | Arthropoda | Insecta | Lepidoptera | Geometridae | FAMILY |
| Makrolepidoptera | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Macrolepidoptera | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Microlepidoptera | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Zygaenidae | Animalia | Arthropoda | Insecta | Lepidoptera | Zygaenidae | FAMILY |
| Sphingidae | Animalia | Arthropoda | Insecta | Lepidoptera | Sphingidae | FAMILY |
| Sesiidae | Animalia | Arthropoda | Insecta | Lepidoptera | Sesiidae | FAMILY |
| Psychidae | Animalia | Arthropoda | Insecta | Lepidoptera | Psychidae | FAMILY |
| Pterophoridae | Animalia | Arthropoda | Insecta | Lepidoptera | Pterophoridae | FAMILY |
| Alucitidae | Animalia | Arthropoda | Insecta | Lepidoptera | Alucitidae | FAMILY |
| Crambidae | Animalia | Arthropoda | Insecta | Lepidoptera | Crambidae | FAMILY |
| Torticidae | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Choreutidae | Animalia | Arthropoda | Insecta | Lepidoptera | Choreutidae | FAMILY |
| Hawk Moths | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Bombycidae | Animalia | Arthropoda | Insecta | Lepidoptera | Bombycidae | FAMILY |
| Pantheidae | Animalia | Arthropoda | Insecta | Lepidoptera | Noctuidae | FAMILY |
| Nolidae | Animalia | Arthropoda | Insecta | Lepidoptera | Nolidae | FAMILY |
| Sessidae | Animalia | Arthropoda | Insecta | Lepidoptera | ||
| Erebidae | Animalia | Arthropoda | Insecta | Lepidoptera | Erebidae | FAMILY |
| Mantodea | Animalia | Arthropoda | Insecta | Mantodea | ORDER | |
| Mecoptera | Animalia | Arthropoda | Insecta | Mecoptera | ORDER | |
| Scorpionflies | Animalia | Arthropoda | Insecta | Mecoptera | ||
| Megaloptera | Animalia | Arthropoda | Insecta | Megaloptera | ||
| Neuroptera | Animalia | Arthropoda | Insecta | Neuroptera | ORDER | |
| Owlflies | Animalia | Arthropoda | Insecta | Neuroptera | ||
| Net-Winged Insects | Animalia | Arthropoda | Insecta | Neuroptera | ||
| Odonata | Animalia | Arthropoda | Insecta | Odonata | ORDER | |
| Orthoptera | Animalia | Arthropoda | Insecta | Orthoptera | ORDER | |
| Grasshoppers | Animalia | Arthropoda | Insecta | Orthoptera | ||
| Ensifera | Animalia | Arthropoda | Insecta | Orthoptera | ||
| Caelifera | Animalia | Arthropoda | Insecta | Orthoptera | ||
| Crickets | Animalia | Arthropoda | Insecta | Orthoptera | ||
| Katydids | Animalia | Arthropoda | Insecta | Orthoptera | ||
| Stick Insects | Animalia | Arthropoda | Insecta | Phasmatodea | ||
| Stoneflies | Animalia | Arthropoda | Insecta | Plecoptera | ||
| Snakeflies | Animalia | Arthropoda | Insecta | Raphidioptera | ||
| Thrips | Animalia | Arthropoda | Insecta | Thysanoptera | Thripidae | GENUS |
| Trichoptera | Animalia | Arthropoda | Insecta | Trichoptera | ORDER | |
| Caddisflies | Animalia | Arthropoda | Insecta | Trichoptera | ||
| Plecoptera | Animalia | Arthropoda | Insecta | CLASS | ||
| Insects | Animalia | Arthropoda | Insecta | |||
| Aquatic and Semi-Aquatic Bugs | Animalia | Arthropoda | Insecta | |||
| Insecta | Animalia | Arthropoda | Insecta | CLASS | ||
| Water Bugs | Animalia | Arthropoda | Insecta | |||
| Woodlice | Animalia | Arthropoda | Isopoda | |||
| Amphipoda | Animalia | Arthropoda | Malacostraca | Amphipoda | ORDER | |
| Niphargidae | Animalia | Arthropoda | Malacostraca | Amphipoda | Niphargidae | FAMILY |
| Cumacea | Animalia | Arthropoda | Malacostraca | Cumacea | ORDER | |
| Decapoda | Animalia | Arthropoda | Malacostraca | Decapoda | ORDER | |
| Crayfishes | Animalia | Arthropoda | Malacostraca | Decapoda | ||
| Astacoidea | Animalia | Arthropoda | Malacostraca | Decapoda | ||
| Freshwater Decapod Crustaceans | Animalia | Arthropoda | Malacostraca | Decapoda | ||
| Marine Decapod Crustaceans | Animalia | Arthropoda | Malacostraca | Decapoda | ||
| Marine Isopoda | Animalia | Arthropoda | Malacostraca | Isopoda | ||
| Malacostraca | Animalia | Arthropoda | Malacostraca | CLASS | ||
| Mysidacea | Animalia | Arthropoda | Malacostraca | CLASS | ||
| Barnacles | Animalia | Arthropoda | Thecostraca | |||
| Freshwater Crabs | Animalia | Arthropoda | Decapoda | |||
| Horseshoe Crabs | Animalia | Arthropoda | Xiphosura | |||
| Crustaceans | Animalia | Arthropoda | ||||
| Arthropods | Animalia | Arthropoda | ||||
| Freshwater Crustaceans | Animalia | Arthropoda | ||||
| Crayfish | Animalia | Arthropoda | ||||
| Sea Spiders | Animalia | Arthropoda | ||||
| Marine Crustaceans | Animalia | Arthropoda | ||||
| Miscellaneous Arthropods | Animalia | Arthropoda | ||||
| Myriapods | Animalia | Arthropoda | ||||
| Brachiopods | Animalia | Brachiopoda | ||||
| Marine Bryozoans | Animalia | Bryoza | ||||
| Bryozoa | Animalia | Bryozoa | PHYLUM | |||
| Bony Fishes | Animalia | Chordata | Actinopterygii | |||
| Frogs | Animalia | Chordata | Amphibia | Anura | ||
| Amphibians | Animalia | Chordata | Amphibia | |||
| Sea Squirts | Animalia | Chordata | Ascidiacea | |||
| Anatidae | Animalia | Chordata | Aves | Anseriformes | Anatidae | FAMILY |
| Galliformes | Animalia | Chordata | Aves | Galliformes | ORDER | |
| Birds | Animalia | Chordata | Aves | |||
| Breeding Birds | Animalia | Chordata | Aves | |||
| Wintering Birds | Animalia | Chordata | Aves | |||
| Transient Birds | Animalia | Chordata | Aves | |||
| Birds Terre Adelie | Animalia | Chordata | Aves | |||
| Birds Terres Australes | Animalia | Chordata | Aves | |||
| Birds Scattered Islands | Animalia | Chordata | Aves | |||
| Migratory Birds | Animalia | Chordata | Aves | |||
| Metropolitan Birds | Animalia | Chordata | Aves | |||
| Endemic Brids | Animalia | Chordata | Aves | |||
| Breeding Birds of Prey | Animalia | Chordata | Aves | |||
| Endangered Birds | Animalia | Chordata | Aves | |||
| Birds Ecuador | Animalia | Chordata | Aves | |||
| Birds Galapagos | Animalia | Chordata | Aves | |||
| Birds of Prey | Animalia | Chordata | Aves | |||
| Breeding Raptors | Animalia | Chordata | Aves | |||
| Freshwater Lamprey | Animalia | Chordata | Cephalaspidomorphi | |||
| Sharks | Animalia | Chordata | Chondrichthyes | |||
| Chondrichthyes | Animalia | Chordata | Chondrichthyes | |||
| Lamprey | Animalia | Chordata | Hyperoartia | |||
| Cetaceans | Animalia | Chordata | Mammalia | Artiodactyla | ||
| Bats | Animalia | Chordata | Mammalia | Chiroptera | ||
| Perissodactyla | Animalia | Chordata | Mammalia | Perissodactyla | ORDER | |
| Primates | Animalia | Chordata | Mammalia | Primates | ORDER | |
| Lemurs | Animalia | Chordata | Mammalia | Primates | ||
| Rodents | Animalia | Chordata | Mammalia | Rodentia | ||
| Mammals | Animalia | Chordata | Mammalia | |||
| Terrestrial Mammals | Animalia | Chordata | Mammalia | |||
| Marine Mammals | Animalia | Chordata | Mammalia | |||
| Mammals Scattered Islands | Animalia | Chordata | Mammalia | |||
| Terrestial Mammals | Animalia | Chordata | Mammalia | |||
| Aquatic Mammals | Animalia | Chordata | Mammalia | |||
| Metropolitan Mammals | Animalia | Chordata | Mammalia | |||
| Endemic Mammals | Animalia | Chordata | Mammalia | |||
| Large Mammals | Animalia | Chordata | Mammalia | |||
| Insectivores | Animalia | Chordata | Mammalia | |||
| Carnivores | Animalia | Chordata | Mammalia | |||
| Marine Cetartiodactyla | Animalia | Chordata | Mammalia | |||
| Terrestrial Cetartiodactyla | Animalia | Chordata | Mammalia | |||
| Proboscidea & Sirenia | Animalia | Chordata | Mammalia | |||
| Endangered Mammals | Animalia | Chordata | Mammalia | |||
| Ungulates | Animalia | Chordata | Mammalia | |||
| Land Mammals | Animalia | Chordata | Mammalia | |||
| Caimans | Animalia | Chordata | Reptilia | Crocodilia | ||
| Chameleons | Animalia | Chordata | Reptilia | Squamata | ||
| Lizards and Worm-Lizards | Animalia | Chordata | Reptilia | Squamata | ||
| Snakes | Animalia | Chordata | Reptilia | Squamata | ||
| Marine Turtles | Animalia | Chordata | Reptilia | Testudines | ||
| Turtles | Animalia | Chordata | Reptilia | Testudines | ||
| Sea Turtles | Animalia | Chordata | Reptilia | Testudines | ||
| Reptiles | Animalia | Chordata | Reptilia | |||
| Terrestrial Reptiles | Animalia | Chordata | Reptilia | |||
| Endemic Lizards | Animalia | Chordata | Reptilia | |||
| Endemic Reptiles | Animalia | Chordata | Reptilia | |||
| Fishes | Animalia | Chordata | ||||
| Lampreys | Animalia | Chordata | ||||
| Freshwater Fishes | Animalia | Chordata | ||||
| Marine Fishes | Animalia | Chordata | ||||
| Tunicata | Animalia | Chordata | ||||
| Lancelets | Animalia | Chordata | ||||
| Reef Fishes | Animalia | Chordata | ||||
| Terrestrial Vertebrates | Animalia | Chordata | ||||
| Freshwater and Migratory Fishes | Animalia | Chordata | ||||
| Cyclostomata | Animalia | Chordata | ||||
| Endangered Vertebrates | Animalia | Chordata | ||||
| Endemic Freshwater Fishes | Animalia | Chordata | ||||
| Linefishes | Animalia | Chordata | ||||
| Brackish and Freshwater Fishes | Animalia | Chordata | ||||
| Corals | Animalia | Cnidaria | ||||
| Cnidaria | Animalia | Cnidaria | PHYLUM | |||
| Reef Corals | Animalia | Cnidaria | ||||
| Marine Cnidaria | Animalia | Cnidaria | ||||
| Echinoderms | Animalia | Echinodermata | ||||
| Acorn Worms | Animalia | Hemichordata | Enteropneusta | |||
| Bivalvia | Animalia | Mollusca | Bivalvia | CLASS | ||
| Marine Bivalves | Animalia | Mollusca | Bivalvia | |||
| Mussels | Animalia | Mollusca | Bivalvia | |||
| Musslels | Animalia | Mollusca | Bivalvia | |||
| Cephalopods | Animalia | Mollusca | Cephalopoda | |||
| Gastropoda | Animalia | Mollusca | Gastropoda | CLASS | ||
| Snails | Animalia | Mollusca | Gastropoda | |||
| Marine Snails | Animalia | Mollusca | Gastropoda | |||
| Terrestrial Gastropods | Animalia | Mollusca | Gastropoda | |||
| Freshwater Gastropods | Animalia | Mollusca | Gastropoda | |||
| Mollusca | Animalia | Mollusca | PHYLUM | |||
| Molluscs | Animalia | Mollusca | ||||
| Terrestrial Molluscs | Animalia | Mollusca | ||||
| Non-Marine Molluscs | Animalia | Mollusca | ||||
| Inland Molluscs | Animalia | Mollusca | ||||
| Species-Poor Groups of Marine Molluscs | Animalia | Mollusca | ||||
| Freswater Mollusc | Animalia | Mollusca | ||||
| Extramarine Molluscs | Animalia | Mollusca | ||||
| Nematoda | Animalia | Nematoda | PHYLUM | |||
| Ribbon Worms | Animalia | Nemertea | ||||
| Flatworms | Animalia | Platyhelminthes | Turbellaria | |||
| Porifera | Animalia | Porifera | PHYLUM | |||
| Sea Sponges | Animalia | Porifera | ||||
| Vertebrates | Animalia | chordata | ||||
| Fauna | Animalia | |||||
| Cave Fauna | Animalia | |||||
| Polychaeta | Animalia | KINGDOM | ||||
| Invertebrates | Animalia | |||||
| Fauna_en_higher | Animalia | |||||
| Fauna_nt_lc_dd | Animalia | |||||
| Fauna_en_vu | Animalia | |||||
| Terrestrial Invertebrates | Animalia | |||||
| Aquatic Invertebrates | Animalia | |||||
| Fauna_flagship Species | Animalia | |||||
| Endemic Fauna | Animalia | |||||
| Protected Animals | Animalia | |||||
| Endangered Fauna | Animalia | |||||
| Selected Species | Animalia | |||||
| Marine Species | Animalia | |||||
| Endangered Species | Animalia | |||||
| Marine Invertebrates | Animalia | |||||
| Freshwater Plants | Animalia | |||||
| Flora Visiting Fauna | Animalia | |||||
| Other Invertebrates | Animalia | |||||
| Other Marine Invertebrates | Animalia | |||||
| Marine Fauna | Animalia | |||||
| Endemic Animals | Animalia | |||||
| Vaucheriaceae | Chromista | Ochrophyta | Xanthophyceae | Vaucheriales | Vaucheriaceae | FAMILY |
| Ascomycota | Fungi | Ascomycota | PHYLUM | |||
| Agaricales | Fungi | Basidiomycota | Agaricomycetes | Agaricales | ORDER | |
| Boletaceae | Fungi | Basidiomycota | Agaricomycetes | Boletales | Boletaceae | FAMILY |
| Boletales | Fungi | Basidiomycota | Agaricomycetes | Boletales | ORDER | |
| Russulales | Fungi | Basidiomycota | Agaricomycetes | Russulales | ORDER | |
| Ustilaginales | Fungi | Basidiomycota | Ustilaginomycetes | Ustilaginales | ORDER | |
| Basidiomycota | Fungi | Basidiomycota | PHYLUM | |||
| Fungi | Fungi | KINGDOM | ||||
| Macromycetes | Fungi | |||||
| Mushrooms | Fungi | |||||
| Macrofungi | Fungi | |||||
| Phytoparasitic Small Fungi | Fungi | |||||
| Large Mushrooms | Fungi | |||||
| Lichenicolous Fungus | Fungi | |||||
| Ascomycetes | Fungi | |||||
| Aphyllophorales | Fungi | |||||
| Phytoparasitic Microfungi | Fungi | |||||
| Characeae | Plantae | Charophyta | Charophyceae | Charales | Characeae | FAMILY |
| Charophyceae | Plantae | Charophyta | Charophyceae | CLASS | ||
| Desmidiales | Plantae | Charophyta | Conjugatophyceae | Desmidiales | ORDER | |
| Zygnematophyceae | Plantae | Charophyta | Zygnematophyceae | CLASS | ||
| Freshwater Diatoms | Plantae | Gyrista | Bacillariophyceae | |||
| Marchantiophyta | Plantae | Marchantiophyta | PHYLUM | |||
| Apiaceae | Plantae | Tracheophyta | Magnoliopsida | Apiales | Apiaceae | FAMILY |
| Cactaceae | Plantae | Tracheophyta | Magnoliopsida | Caryophyllales | Cactaceae | FAMILY |
| Magnoliaceae | Plantae | Tracheophyta | Magnoliopsida | Magnoliales | Magnoliaceae | FAMILY |
| Anisoptera | Plantae | Tracheophyta | Magnoliopsida | Malvales | Dipterocarpaceae | GENUS |
| Dipterocarpaceae | Plantae | Tracheophyta | Magnoliopsida | Malvales | Dipterocarpaceae | FAMILY |
| Magnoliophyta | Plantae | Tracheophyta | PHYLUM | |||
| Charophytes | Plantae | Charophyceae | Charales | |||
| Lycopods | Plantae | Lycopodiopsida | Lycopodiales | |||
| Tree Ferns | Plantae | Polypodiopsida | ||||
| Sphagnum Mosses | Plantae | Sphagnopsida | ||||
| Orchids | Plantae | Asparagales | ||||
| Wild Cinnamon | Plantae | Laurales | ||||
| Bromeliads | Plantae | Poales | ||||
| Flora | Plantae | |||||
| Bryophytes | Plantae | |||||
| Ferns | Plantae | |||||
| Vascular Plants | Plantae | |||||
| Lichens | Plantae | |||||
| Hydrophytes | Plantae | |||||
| Marine Flora | Plantae | |||||
| Hornworts | Plantae | |||||
| Liverworts | Plantae | |||||
| Mosses | Plantae | |||||
| Flora Saint Paul and Amsterdam | Plantae | |||||
| Flora Scattered Islands | Plantae | |||||
| Flora Kerguelen | Plantae | |||||
| Endemic Flora | Plantae | |||||
| Trees | Plantae | |||||
| Shrubs | Plantae | |||||
| Algae | Plantae | |||||
| Arctic Vascular Plants | Plantae | |||||
| Marine Macroalgae | Plantae | |||||
| Freshwater Red Algae | Plantae | |||||
| Freshwater Brown Algae | Plantae | |||||
| Flowering Plant | Plantae | |||||
| Red Algae | Plantae | |||||
| Brown Algae | Plantae | |||||
| Hepaticophyta | Plantae | |||||
| Broad-Leaved Mosses | Plantae | |||||
| Lichen Communities | Plantae | |||||
| Flora of Cerrado Biom | Plantae | |||||
| Endemic Plants | Plantae | |||||
| Flora On the Red List | Plantae | |||||
| Protected Plants | Plantae | |||||
| Endangered Plants | Plantae | |||||
| Near-Endemic Flora | Plantae | |||||
| Perennial Shrubs | Plantae | |||||
| Flora_2 | Plantae | |||||
| Endemic and Range-Restricted Vascular Plantss | Plantae | |||||
| Indigenous Plants | Plantae | |||||
| Selected Species In Marshlands | Plantae | |||||
| Conifers | Plantae | |||||
| Peninsular Planrs | Plantae | |||||
| Lycophytes | Plantae | |||||
| Higher Plants | Plantae | |||||
| Cloud Forest Trees | Plantae | |||||
| Spermatophytes | Plantae | |||||
| Palms | Plantae | |||||
| Wild Crop Relatives | Plantae | |||||
| Aquatic Plants | Plantae | |||||
| Medicinal Plants | Plantae | |||||
| Dry Forest Trees | Plantae | |||||
| Monocotyledons | Plantae | |||||
| Freshwater Flora | Plantae | |||||
| Flora List | Plantae | |||||
| Endemic Trees | Plantae | |||||
| Myxomycetes | Protozoa | Mycetozoa | Myxomycetes | CLASS | ||
| Protozoa | Protozoa | KINGDOM | ||||
| Zygoptera | Protozoa | GENUS |
Check Event fields
The fields is: year
- Check it has numeric values.
raw_metadata %>%
janitor::clean_names() %>%
janitor::remove_empty(c('rows', 'cols')) %>%
select(year, name_orig) %>%
mutate(year = ifelse(year == 'NA', NA, year)) %>%
mutate(year_new = as.numeric(year, na.rm=T)) %>%
filter(is.na(year_new)) %>%
distinct(name_orig, .keep_all = T)
raw_metadata %>%
janitor::clean_names() %>%
janitor::remove_empty(c('rows', 'cols')) %>%
mutate(year = ifelse(year == 'NA', NA, year)) %>%
mutate(year = ifelse(year == '2024?', 2024, year)) %>%
mutate(year = as.numeric(year, na.rm=T)) %>%
mutate(year = case_when(is.na(year) &
name_orig == 'Crveni popis hrvatskih koralja'
~ 2024,
is.na(year) &
name_orig == 'A Red List of Benin’s sharks'
~ 2024,
is.na(year) &
name_orig == 'Crveni popis lišajeva Hrvatske'
~ 2024,
is.na(year) &
name_orig == 'Červené seznamy'
~ 2024,
is.na(year) &
name_orig == 'Coleoptera (Beetle) – Invertebrate Ireland Online'
~ 2024,
is.na(year) &
name_orig == 'Tricoptera (Caddisfly) – InvertebrateIreland Online'
~ 2024,
is.na(year) &
name_orig == 'Les mammifères de la Côte d’Ivoire'
~ 2024,
is.na(year) &
name_orig == 'Rongeurs et insectivores de Côte d’Ivoire, leur habitat et leur statut de conservation'
~ 2024,
is.na(year) &
name_orig == 'Красная книга Азербайджанской Республики'
~ 2024,
is.na(year) &
name_orig == 'Красная книга Узбекистана'
~ 2024,
.default = year)) %>%
# filter(is.na(year)) %>%
select(year, name_orig) %>%
distinct(name_orig, .keep_all = T) DOUBTS
https://www.odonat-grandest.fr/listes-rouges-grand-est-etat-avancement/
A Red List of Benin’s sharks
The Red List of Mammals of South Africa, Swaziland and Lesotho 2024
1 Crveni popis hrvatskih koralja
2 Crveni popis lišajeva Hrvatske
3 Červené seznamy
4 Coleoptera (Beetle) – Invertebrate Ireland Online
5 Tricoptera (Caddisfly) – InvertebrateIreland Online
6 Les mammifères de la Côte d’Ivoire
7 Rongeurs et insectivores de Côte d’Ivoire, leur habitat et leur statut de conservation
8 Красная книга Азербайджанской Республики
9 Красная книга Узбекистана
Check if URLs are working
# URL incorrect
raw_metadata %>%
filter(!grepl('http', url_clean)) %>%
distinct(url_clean)# A tibble: 3 × 1
url_clean
<chr>
1 NA
2 ima.sc.gov.br/index.php/biodiversidade/biodiversidade/fauna
3 <NA>
# URL error
# raw_metadata %>% filter(grepl('http', url_clean)) %>%
# distinct(url_clean) %>%
# mutate(check_URL = ifelse(map(URLencode(url_clean), http_error), 'not found', 'OK')) %>%
# filter(check_URL == 'not found') DOUBTS
ima.sc.gov.br/index.php/biodiversidade/biodiversidade/fauna
Nicolau, J. i Dalmau, J., 2008. Llista Vermella\r\ndels Vertebrats d’Andorra. BIOCOM (Biologia i\r\nComunicació) SL i Departament de Patrimoni\r\nNatural del Govern d’Andorra. Informe inèdit
Run code and keep relevant fields
metadata <-
# check taxon
left_join(raw_metadata %>% mutate(group = str_trim(group)) %>%
select(-c(kingdom,phylum,subphylum,class,order)),
bind_rows(merged_list %>% filter(!is.na(scientificName)),
merged_list %>% filter(is.na(scientificName)) %>%
select(group) %>%
left_join(. , raw_metadata_taxon_list))) %>%
mutate(group = str_trim(group)) %>%
mutate(group = str_to_title(group)) %>%
mutate(group = str_replace_all(group, 'And ', 'and ')) %>%
mutate(group = str_replace_all(group, 'Of', 'of')) %>%
mutate(group = str_replace_all(group, 'The', 'the')) %>%
# more taxonomic corrections
#
#
#
#
# check columns
janitor::clean_names() %>%
janitor::remove_empty(c('rows', 'cols')) %>%
# check source
mutate(name_orig = str_squish(name_orig)) %>%
mutate(name_orig = str_remove_all(name_orig, "\\\\")) %>%
mutate(name_orig = str_remove_all(name_orig, "\"")) %>%
mutate(name_orig = ifelse(grepl('htt', name_orig) &
state_province == 'Grand Est',
str_glue('Red list of {group} of Grand Est'), name_orig)) %>%
# missing name of source
# check format
mutate(format = ifelse(format == 'NA', NA, str_squish(format))) %>%
mutate(format = ifelse(format == '?', NA, format)) %>%
# check language
mutate(language = ifelse(language == 'NA', NA, str_squish(language))) %>%
mutate(language = str_replace(language, "/|\\|", ' | ')) %>%
# check location
mutate(continent = str_squish(str_replace_all(str_squish(continent), '\\|', ' | '))) %>%
mutate(continent = str_replace_all(continent, '_', ' ')) %>%
mutate(continent = str_to_title(continent)) %>%
mutate(country = ifelse(country == 'NA', NA, str_squish(country))) %>%
mutate(country = str_replace_all(country, '_', ' ')) %>%
mutate(country = ifelse(country == 'USSR', country, str_to_title(country))) %>%
mutate(country = str_replace_all(country, 'And ', 'and ')) %>%
mutate(country = str_replace_all(country, 'Of', 'of')) %>%
mutate(country = str_replace_all(country, 'The', 'the')) %>%
mutate(state_province = ifelse(state_province == 'NA', NA, str_squish(state_province))) %>%
mutate(state_province = str_to_title(state_province)) %>%
mutate(iso_2 = ifelse(iso_2 == 'NA' & country != 'Namibia', NA, str_squish(iso_2))) %>%
mutate(iso_3 = ifelse(iso_3 == 'NA', NA, str_squish(iso_3))) %>%
mutate(iso_2 = str_squish(str_replace_all(str_squish(iso_2), '\\|', ' | '))) %>%
mutate(iso_3 = str_squish(str_replace_all(str_squish(iso_3), '\\|', ' | '))) %>%
mutate(gadm_level_1 = ifelse(gadm_level_1 == 'NA', NA, str_squish(gadm_level_1))) %>%
mutate(gadm_level_1 = str_to_title(gadm_level_1)) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'And ', 'and ')) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'Of', 'of')) %>%
mutate(gadm_level_1 = str_replace_all(gadm_level_1, 'The', 'the')) %>%
mutate(gadm_level_2 = ifelse(gadm_level_2 == 'NA', NA, str_squish(gadm_level_2))) %>%
mutate(gadm_level_2 = str_to_title(gadm_level_2)) %>%
mutate(region_custom = ifelse(region_custom == 'NA', NA, str_squish(region_custom))) %>%
mutate(region_detail = ifelse(region_detail == 'NA', NA, str_squish(region_detail))) %>%
mutate(region_detail = str_squish(str_replace_all(str_squish(region_detail), '\\|', ' | '))) %>%
# check event
mutate(year = ifelse(year == 'NA', NA, year)) %>%
mutate(year = ifelse(year == '2024?', 2024, year)) %>%
mutate(year = as.numeric(year, na.rm=T)) %>%
mutate(year = case_when(is.na(year) &
name_orig == 'Crveni popis hrvatskih koralja'
~ 2024,
is.na(year) &
name_orig == 'A Red List of Benin’s sharks'
~ 2024,
is.na(year) &
name_orig == 'Crveni popis lišajeva Hrvatske'
~ 2024,
is.na(year) &
name_orig == 'Červené seznamy'
~ 2024,
is.na(year) &
name_orig == 'Coleoptera (Beetle) – Invertebrate Ireland Online'
~ 2024,
is.na(year) &
name_orig == 'Tricoptera (Caddisfly) – InvertebrateIreland Online'
~ 2024,
is.na(year) &
name_orig == 'Les mammifères de la Côte d’Ivoire'
~ 2024,
is.na(year) &
name_orig == 'Rongeurs et insectivores de Côte d’Ivoire, leur habitat et leur statut de conservation'
~ 2024,
is.na(year) &
name_orig == 'Красная книга Азербайджанской Республики'
~ 2024,
is.na(year) &
name_orig == 'Красная книга Узбекистана'
~ 2024,
.default = year)) %>%
# select columns
select(id, continent,
gadm_level_0 = country, gadm_level_1, gadm_level_2,
region_custom, region_detail, iso_2, iso_3,
taxa=group, kingdom, phylum, class, order, family,
url = url_clean, source_name= name_orig,
language, year)
metadata %>% slice_sample(n=50) %>% arrange(id) %>%
kableExtra::kbl(booktabs = T) %>%
kableExtra::kable_styling(latex_options = c('striped', 'hold_position'))| id | continent | gadm_level_0 | gadm_level_1 | gadm_level_2 | region_custom | region_detail | iso_2 | iso_3 | taxa | kingdom | phylum | class | order | family | url | source_name | language | year |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 57 | Europe | Austria | Oberösterreich | AT | AUT | Grasshoppers | Animalia | Arthropoda | Insecta | Orthoptera | https://www.zobodat.at/pdf/BNO_0014_0027-0037.pdf | Die Heuschreckenfauna ausgewählter Halbtrockenrasen des Strudengaus und des angrenzenden unteren Mühlviertels (Oberösterreich) | Deutsch | 2005 | ||||
| 171 | Europe | Romania | RO | ROU | Characeae | Plantae | Charophyta | Charophyceae | Charales | Characeae | https://link.springer.com/article/10.1007/s10531-005-2008-5 | Red Data List of Charophytes in the Balkans | English | 2006 | ||||
| 243 | Europe | Slovenia | SI | SVN | Protozoa | Protozoa | https://www.uradni-list.si/files/RS_-2002-082-04055-OB~P041-0000.PDF | Rdeči seznam praživali (Protozoa) | Slovenian | 2002 | ||||||||
| 250 | Europe | Italy | IT | ITA | Flora | Plantae | https://arts.units.it/bitstream/11368/2964383/2/10.1080%4011263504.2020.1739165.pdf | Red list of threatened vascular plants in Italy | English | 2020 | ||||||||
| 260 | Europe | Italy | IT | ITA | Flora | Plantae | https://www.iucn.it/pdf/Comitato_IUCN_Lista_Rossa_della_flora_italiana_policy_species.pdf | Lista Rossa de la Flora Italiana 1. POLICY SPECIES e altre specie minacciate | Italian | 2013 | ||||||||
| 272 | Europe | Switzerland | CH | CHE | Mammals | Animalia | Chordata | Mammalia | https://www.bafu.admin.ch/bafu/de/home/themen/biodiversitaet/publikationen-studien/publikationen/rote-listen-saeugetiere.html | Rote Liste der Säugetiere (ohne Fledermäuse). Gefährdete Arten der Schweiz. | German | 2022 | ||||||
| 326 | Europe | Malta | MT | MLT | Flora | Plantae | https://era.org.mt/red-data-book-for-the-maltese-islands/ | Red data book for the Maltese Islands | English | 1989 | ||||||||
| 357 | Africa | Réunion | RE | REU | Reef Fishes | Animalia | Chordata | https://inpn.mnhn.fr/espece/listerouge/FR/Poissons_recifaux_Reunion_2022 | Liste rouge des poissons de récif de la Réunion (France) | French | 2022 | |||||||
| 400 | Africa | French Southern Territories | TF | ATF | Reptiles | Animalia | Chordata | Reptilia | https://inpn.mnhn.fr/espece/listerouge/FR/Reptiles_Eparses_TAAF_2015 | Liste rouge des reptiles des îles Éparses (France) | French | 2015 | ||||||
| 420 | Europe | France | Bretagne | FR | FRA | Flora | Plantae | https://inpn.mnhn.fr/espece/programme/listes-rouges/RG/?region=INSEER53 | Liste rouge de la Flore de Bretagne | French | 2015 | |||||||
| 441 | Europe | France | Corse | FR | FRA | Butterflies | Animalia | Arthropoda | Insecta | Lepidoptera | https://inpn.mnhn.fr/docs/LR_FCE/LR_regionale/Corse/LRR_Rhopaloceres_Zygenes_Corse_2017.pdf | Liste rouge des Papillons diurnes de Corse | French | 2017 | ||||
| 449 | Europe | France | Grand Est | FR | FRA | Fishes | Animalia | Chordata | https://www.odonat-grandest.fr/listes-rouges-grand-est-etat-avancement/ | Red list of Fishes of Grand Est | French | 2024 | ||||||
| 486 | Europe | France | Occitania | FR | FRA | Orthoptera | Animalia | Arthropoda | Insecta | Orthoptera | https://www.occitanie.developpement-durable.gouv.fr/listes-rouges-regionales-occitanie-a24640.html?lang=fr | Liste rouge des Orthoptères d'Occitanie | French | 2022 | ||||
| 519 | Europe | France | Aquitaine | FR | FRA | Mammals | Animalia | Chordata | Mammalia | https://www.nouvelle-aquitaine.developpement-durable.gouv.fr/les-listes-rouges-regionales-a9991.html?lang=fr | Liste rouge des mammifères continentaux non volants d'Aquitaine | French | 2020 | |||||
| 579 | Europe | France | Nord-Pas-De-Calais | FR | FRA | Reptiles | Animalia | Chordata | Reptilia | https://inpn.mnhn.fr/docs/LR_FCE/LR_regionale/Nord-Pas-de-Calais/LRR_Amphibiens_Reptiles_NPDC.pdf | Liste rouge régionale – Nord – Pas-de-Calais - Les Amphibiens et Reptiles du Nord - Pas-de-Calais | French | 2015 | |||||
| 610 | Europe | Bulgaria | BG | BGR | Fauna_en_higher | Animalia | http://e-ecodb.bas.bg/rdb/en/vol2/texts.html | Red Data Book of the Republic of Bulgaria. Vol. 2. Animals | English | 2011 | ||||||||
| 655 | Europe | Hungary | HU | HUN | Trees | Plantae | https://www.researchgate.net/publication/341616466_Voros_Lista_Magyarorszag_veszelyeztetett_fa-_es_cserjefajai_Red_List_Threatened_tree_and_shrub_species_of_Hungary_-_Soproni_Egyetem_Kiado_University_of_Sopron_Press_Sopron_2019_59_pp | Vörös Lista. Magyarország veszélyeztetett fa- és cserjefajai | Hungarian | 2019 | ||||||||
| 689 | Europe | United Kingdom | GB | GBR | Larger Brachycera | Animalia | Arthropoda | Insecta | Diptera | https://publications.naturalengland.org.uk/publication/5411344246374400?category=4707656804597760 | A review of the status of larger Brachycera flies of Great Britain (NECR192) | English | 2017 | |||||
| 801 | Europe | Sweden | Gästrikland | SE | SWE | Fauna | Animalia | https://artfakta.se/sok | SLU Artdatabanken (2020). Rödlista 2020 | Swedish | 2020 | |||||||
| 928 | Europe | Germany | DE | DEU | Odonata | Animalia | Arthropoda | Insecta | Odonata | https://www.rote-liste-zentrum.de/en/Download-Vertebrates-1874.html | Rote Liste und Gesamtartenliste der Libellen (Odonata) Deutschlands | German | 2021 | |||||
| 999 | Europe | Germany | Baden-Württemberg | DE | DEU | Odonata | Animalia | Arthropoda | Insecta | Odonata | https://www.lubw.baden-wuerttemberg.de/natur-und-landschaft/rote-listen | Rote Liste der Libellen Baden-Württembergs und der Naturräume | German | 2005 | ||||
| 1041 | Europe | Germany | Bayern | DE | DEU | Lamellicornia | Animalia | Arthropoda | Insecta | Coleoptera | https://www.lfu.bayern.de/natur/rote_liste_tiere/2003/index.htm | Rote Liste gefährdeter Blatthornkäfer (Coleoptera: Lamellicornia) Bayerns | German | 2003 | ||||
| 1176 | Europe | Germany | Brandenburg | DE | DEU | Odonata | Animalia | Arthropoda | Insecta | Odonata | https://lfu.brandenburg.de/lfu/de/ueber-uns/veroeffentlichungen/detail/~08-09-2017-zeitschrift-naturschutz-und-landschaftspflege-in-brandenburg-beilage-zu-heft-4-2017 | Rote Liste der Libellen (Odonata) des Landes Brandenburg 2016 | German | 2016 | ||||
| 1249 | Europe | Germany | Bremen | DE | DEU | Stoneflies | Animalia | Arthropoda | Insecta | Plecoptera | https://www.nlwkn.niedersachsen.de/naturschutz/rote-liste-der-eintags-stein-und-kocherfliegenarten-niedersachsens-38879.html | Rote Liste der Eintags-, Stein- und Köcherfliegenarten Niedersachsens | German | 2000 | ||||
| 1256 | Europe | Germany | Niedersachsen | DE | DEU | Heteroptera | Animalia | Arthropoda | Insecta | Diptera | Sphaeroceridae | https://www.nlwkn.niedersachsen.de/naturschutz/rote-liste-der-in-niedersachsen-und-bremen-gefahrdeten-wanzen-38884.html | Rote Liste der in Niedersachsen und Bremen gefährdeten Wanzen | German | 1999 | |||
| 1257 | Europe | Germany | Bremen | DE | DEU | Spiders | Animalia | Arthropoda | Arachnida | Araneae | https://www.nlwkn.niedersachsen.de/naturschutz/rote-liste-der-in-niedersachsen-und-bremen-gefahrdeten-webspinnen-mit-gesamtartenverzeichnis-38796.html | Rote Liste der in Niedersachsen und Bremen gefährdeten Webspinnen mit Gesamtartenverzeichnis | German | 2004 | ||||
| 1378 | Europe | Germany | Mecklenburg-Vorpommern | DE | DEU | Snails | Animalia | Mollusca | Gastropoda | https://www.lung.mv-regierung.de/fachinformationen/natur-und-landschaft/artenschutz/rote-listen/ | Rote Liste der gefährdeten Schnecken und Muscheln des Binnenlandes Mecklenburg-Vorpommerns | German | 2002 | |||||
| 1418 | Europe | Germany | Nordrhein-Westfalen | DE | DEU | Red Algae | Plantae | https://www.lanuk.nrw.de/themen/natur/artenschutz/rote-liste | Rote Liste und Artenverzeichnis der Rot- und Braunalgen - Rhodophyceae et Fucophyceae - in NRW, 1. Fassung | German | 2010 | |||||||
| 1457 | Europe | Germany | Saarland | DE | DEU | Bats | Animalia | Chordata | Mammalia | Chiroptera | https://rote-liste-saarland.de/ | Rote Liste und Gesamtartenliste der Fledermäuse (Chiroptera) des Saarlandes | German | 2020 | ||||
| 1541 | Europe | Germany | Sachsen | DE | DEU | Spiders | Animalia | Arthropoda | Arachnida | Araneae | https://publikationen.sachsen.de/bdb/artikel/39282 | Rote Liste Weberknechte und Webspinnen | German | 1996 | ||||
| 1608 | Europe | Germany | Sachsen-Anhalt | DE | DEU | Cerophytidae | Animalia | Arthropoda | Insecta | Coleoptera | Cerophytidae | https://lau.sachsen-anhalt.de/alt-vor-neuer-navigation/wir-ueber-uns-publikationen/fachpublikationen/berichte-des-lau/rote-listen-sachsen-anhalt-2040 | Rote Listen Sachsen-Anhalt 2020 | German | 2020 | |||
| 1612 | Europe | Germany | Sachsen-Anhalt | DE | DEU | Latridiidae | Animalia | Arthropoda | Insecta | Coleoptera | Latridiidae | https://lau.sachsen-anhalt.de/alt-vor-neuer-navigation/wir-ueber-uns-publikationen/fachpublikationen/berichte-des-lau/rote-listen-sachsen-anhalt-2044 | Rote Listen Sachsen-Anhalt 2020 | German | 2020 | |||
| 1625 | Europe | Germany | Sachsen-Anhalt | DE | DEU | Orsodacnidae | Animalia | Arthropoda | Insecta | Coleoptera | Orsodacnidae | https://lau.sachsen-anhalt.de/alt-vor-neuer-navigation/wir-ueber-uns-publikationen/fachpublikationen/berichte-des-lau/rote-listen-sachsen-anhalt-2047 | Rote Listen Sachsen-Anhalt 2020 | German | 2020 | |||
| 1784 | Europe | Germany | Thüringen | DE | DEU | Leiodidae | Animalia | Arthropoda | Insecta | Coleoptera | Leiodidae | https://tlubn.thueringen.de/naturschutz/rote-listen/kaefer | Rote Liste der Aaskäfer, Nestkäfer, Poch- und Diebskäfer, Scheinbockkäfer, Ölkäfer, Düsterkäfer, Schwarzkäfer (Insecta: Coleoptera: Silphidae, Leiodidae pt., Ptinidae, Oedemeridae, Meloidae, Melandryidae, Tenebrionidae) und weiterer ausgewählter Käferfamilien Thüringens 2020 | German | 2020 | |||
| 1785 | Europe | Germany | Thüringen | DE | DEU | Ptinidae | Animalia | Arthropoda | Insecta | Coleoptera | Ptinidae | https://tlubn.thueringen.de/naturschutz/rote-listen/kaefer | Rote Liste der Aaskäfer, Nestkäfer, Poch- und Diebskäfer, Scheinbockkäfer, Ölkäfer, Düsterkäfer, Schwarzkäfer (Insecta: Coleoptera: Silphidae, Leiodidae pt., Ptinidae, Oedemeridae, Meloidae, Melandryidae, Tenebrionidae) und weiterer ausgewählter Käferfamilien Thüringens 2020 | German | 2020 | |||
| 1821 | Europe | Germany | Thüringen | DE | DEU | Zygaenidae | Animalia | Arthropoda | Insecta | Lepidoptera | Zygaenidae | https://tlubn.thueringen.de/naturschutz/rote-listen/schmetterlinge | Rote Liste der Widderchen (Insecta: Lepidoptera: Zygaenidae) Thüringens 2010 | German | 2010 | |||
| 1898 | Europe | Liechtenstein | LI | LIE | Reptiles | Animalia | Chordata | Reptilia | https://www.llv.li/serviceportal2/amtsstellen/amt-fuer-umwelt/publikationen/naturkindliche-forschung/b23-reptilien.pdf | Die Reptilien des Fürstentums Liechtenstein | German | 2006 | ||||||
| 2102 | Asia | South Korea | KR | KOR | Endangered Mammals | Animalia | Chordata | Mammalia | https://www.researchgate.net/publication/330162745_Mammals_of_Korea | MAMMALS OF KOREA | English | 1997 | ||||||
| 2191 | Asia | Georgia | GE | GEO | Fauna | Animalia | https://environment.cenn.org/ge/%E1%83%92%E1%83%90%E1%83%93%E1%83%9B%E1%83%9D%E1%83%AC%E1%83%94%E1%83%A0%E1%83%90/%E1%83%A1%E1%83%90%E1%83%A5%E1%83%90%E1%83%A0%E1%83%97%E1%83%95%E1%83%94%E1%83%9A%E1%83%9D%E1%83%A1-%E1%83%AC%E1%83%98%E1%83%97%E1%83%94%E1%83%9A%E1%83%98-%E1%83%AC%E1%83%98%E1%83%92%E1%83%9C%E1%83%98/ | საქართველოს წითელი წიგნი | Georgian | 1982 | ||||||||
| 2205 | Asia | Kyrgyzstan | KG | KGZ | Flora | Plantae | http://oopt-back.at.kg/uploads/publication/Red_Book_KR.pdf | KYRGYZ REPUBLIC RED DATA BOOK (SECOND EDITION) | Kyrgyz | 2006 | ||||||||
| 2227 | Asia | Thailand | TH | THA | Birds | Animalia | Chordata | Aves | https://patricklepetit.jalbum.net/_FAUNA%20OF%20THAILAND/LIBRARY/Birds%20of%20Thailand.pdf | Thailand Red Data : Birds | English | 2005 | ||||||
| 2346 | Europe | Belgium | Vlaanderen | BE | BEL | Flora | Plantae | https://www.vlaanderen.be/inbo/rode-lijsten/ | Vlaanderen Instituut voor Natuur- en Bosonderzoek - Rode lijsten | Dutch | 2024 | |||||||
| 2407 | Europe | Netherlands | NL | NLD | Bryophytes | Plantae | https://www.blwg.nl/mossen/onderzoek/rapporten/BLWGRapport14.pdf | Basisrapport voor de Rode Lijst Mossen 2012 | Dutch | 2012 | ||||||||
| 2505 | Europe | Poland | PL | POL | Apoidea | Animalia | Arthropoda | Insecta | Hymenoptera | https://rcin.org.pl/iop/dlibra/publication/90278 | Czerwona lista zwierząt ginących i zagrożonych w Polsce: Pszczoły Apoidea | Polish | 1992 | |||||
| 2566 | North America | United States Virgin Islands | VI | VIR | Flora | Plantae | https://dpnr.vi.gov/wp-content/uploads/2022/10/VI-WAP-Vol-2-Habitats-Species.pdf | United States Virgin Islands Wildlife Action Plan | English | 2018 | ||||||||
| 2647 | South America | Chile | CL | CHL | Flora | Plantae | http://especies.mma.gob.cl/CNMWeb/Web/WebCiudadana/especies_amenazadas.aspx | Especies Amenazadas de Chile | Spanish | 2024 | ||||||||
| 2703 | South America | Peru | PE | PER | Cactaceae | Plantae | Tracheophyta | Magnoliopsida | Caryophyllales | Cactaceae | http://www.scielo.org.pe/pdf/rpb/v13n2/v13n02a027.pdf | Cactaceae endémicas del Perú | Spanish | 2006 | ||||
| 2955 | Asia | Japan | JP | JPN | Birds | Animalia | Chordata | Aves | https://ikilog.biodic.go.jp/Rdb/booklist | レッドリスト2012 | Japanese | 2012 | ||||||
| 3046 | Europe | Russia | Adygey | RU | RUS | Flora | Plantae | https://www.plantarium.ru/lang/en/page/redbook/id/322.html | Красная книга Республики Адыгея, 2021 г. | Russian | 2021 | |||||||
| 3105 | Europe | Russia | Ivanovo | RU | RUS | Fungi | Fungi | https://rusmam.ru/static/literature/2f/eb/2feb859ebc6b2ab99deed732f215a874.pdf | Красная книга Ивановской области. Т. 1 | Russian | 2010 |
Data audit
Summary
Code
metadata %>%
summarise(`Number of records` = n(),
`Number of sources` = n_distinct(source_name),
`Number of taxa` = n_distinct(taxa),
`Animalia records` = sum(kingdom == 'Animalia'),
`Plantae records` = sum(kingdom == 'Plantae'),
`Fungi records` = sum(kingdom == 'Fungi'),
Countries = n_distinct(gadm_level_0),
`Sub-national territories` = n_distinct(gadm_level_1)) %>%
t() %>% `colnames<-`(c("N")) %>%
kableExtra::kbl(booktabs = T) %>%
kableExtra::kable_styling(latex_options = c('striped', 'hold_position'))| N | |
|---|---|
| Number of records | 3200 |
| Number of sources | 2093 |
| Number of taxa | 487 |
| Animalia records | 2190 |
| Plantae records | 898 |
| Fungi records | 105 |
| Countries | 171 |
| Sub-national territories | 223 |
Geographic coverage
Code
world <- geodata::world(resolution = 3, level = 0, path = 'data/')
world_records <- left_join(st_as_sf(world), metadata %>%
separate_rows(iso_3, sep = '\\|') %>%
select(iso_2, GID_0=iso_3, source_name)) %>%
group_by(GID_0, NAME_0) %>%
summarise(n_records = ifelse(n_distinct(source_name, na.rm = TRUE)==0,
0, n_distinct(source_name, na.rm = TRUE)),
iso_2_string = ifelse(n_records>0,
paste(iso_2, collapse = ';'), NA))
plot_figure_1 <- tm_shape(world_records %>%
select(-iso_2_string) %>%
mutate(n_records=ifelse(n_records==0,
NA, n_records))) +
tm_polygons(fill = 'n_records',fill_alpha = 0.9,
col='grey40', col_alpha = 0.2,
fill.scale = tm_scale_intervals(n = 6,
#style = 'jenks',
breaks = c(1,5,10,20,100,979),
values = 'brewer.reds',
value.na = 'grey80',
label.na = '0'),
fill.legend = tm_legend(item.space = 0, item.na.space = 0,
title = 'Number of sources',
reverse=T,
# frame=F,
frame.lwd = 0.1,
bg.color = 'white')) +
tm_layout(legend.outside = T,
legend.position = c('left','bottom'), frame=F) +
tm_crs(property='global')
tmap_mode('plot')
plot_figure_1Code
tmap_mode('view')
plot_figure_1